AMBER Archive (2006)

Subject: RE: AMBER: Installation help - SGI Altix 350

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Dec 20 2006 - 23:30:53 CST

Dear Bertrand,
 
This sounds like an issue with the way your system is setup and how jobs are
submitted and run in parallel. Do you have a queing system installed? It is
possible that you need to request a certain number of cpus interactively
through your queuing system. I can' treally help you much here without
seeing the machine setup. Do you have an administrator for this machine that
can show you how to run parallel jobs on it?
 
All the best
Ross
 

/\
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|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk <http://www.rosswalker.co.uk/> | PGP Key
available on request |

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  _____

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
bertrand russell
Sent: Wednesday, December 20, 2006 21:10
To: amber_at_scripps.edu
Subject: Re: AMBER: Installation help - SGI Altix 350

Dear Ross,

                Thank you very much for your immediate reply. I issued the
following command as instructed by you. I am getting the following error
message.

############################################################################
#
bash-2.05b$ export DO_PARALLEL='mpirun -np 4'
bash-2.05b$ make test.parallel
export TESTsander=/pludisk1/facs/sanjib/AMBER9/amber9/exe/sander.MPI; make
test.sander.BASIC
make[1]: Entering directory `/pludisk1/facs/sanjib/AMBER9/amber9/test'
cd dmp; ./Run.dmp
This test not set up for parallel
 cannot run in parallel with #residues < #pes
cd adenine; ./Run.adenine
This test not set up for parallel
 cannot run in parallel with #residues < #pes
==============================================================
cd cytosine; ./Run.cytosine
MPI: asgetnetinfo_array('(null)') failed : request failed - authentication
failure
  ./Run.cytosine: Program error
make[1]: *** [test.sander.BASIC] Error 1
make[1]: Leaving directory `/pludisk1/facs/sanjib/AMBER9/amber9/test'
make: *** [test.sander.BASIC.MPI] Error 2

############################################################################
###

What might be the problem?

On 12/21/06, Ross Walker <ross_at_rosswalker.co.uk> wrote:

Hi Bertrand,
 
Ah I see, you need to include quotes. Do the following:
 
cd $AMBERHOME/test/
export DO_PARALLEL='mpirun -np 4'
make test.parallel

 
All the best
Ross

/\
\/
|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk <http://www.rosswalker.co.uk/> | PGP Key
available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

 

  _____

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
bertrand russell
Sent: Wednesday, December 20, 2006 20:13
To: amber_at_scripps.edu
Subject: Re: AMBER: Installation help - SGI Altix 350

Dear Ross,

                  As you suggested I issued >which mpirun command. It showed
/usr/bin/mpirun.

bash-2.05b$ which mpirun
/usr/bin/mpirun

And I am not getting any errors while testing the pararllel. I don't know
how to set the environment pvariable for DO_PARALLEL. Details on this is as
follows,

bash-2.05b$ DO_PARALLEL=mpirun -np 4
bash: -np: command not found
 What should I do to overcome this problem? Many thanks for your reply.

On 12/20/06, Ross Walker < ross_at_rosswalker.co.uk> wrote:

Dear Bertrand,
 
We really need some more information about your system and what you are
doing to be able to help out some more. If things compiled okay - I.e. you
built a parallel version with no errors such that you now have a sander.MPI
executable in your $AMBERHOME/exe/ directory then I suspect there is nothing
wrong with the mpi implementation on your machine.
 
On SGI Altix machines the MPI installation is generally vendor supplied. You
should check which mpirun you have in your path:
 
which mpirun
 
You should see /usr/bin/mpirun
 
Also please show exactly what you are setting for the DO_PARALLEL variable
and exactly what error messages you see when you type make test.parallel.
 
I suspect that for some reason you don't have mpirun defined in your path or
that it points to a non-standard mpi installation.
 
All the best
Ross

/\
\/
|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk <http://www.rosswalker.co.uk/> | PGP Key
available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

 

  _____

From: owner-amber_at_scripps.edu [mailto: <mailto:owner-amber_at_scripps.edu>
owner-amber_at_scripps.edu] On Behalf Of bertrand russell
Sent: Wednesday, December 20, 2006 02:47
To: amber_at_scripps.edu
Subject: AMBER: Installation help - SGI Altix 350

Dear Amber users,

I am trying to install Amber9 in SGI Altix 350 running in SGI pro pack 2. I
have done all the steps successfully till making sander parallel. I now want
to test my parallel version using >make test.parallel. Before that it seems
that I need to set an environmental variable for DO_PARALLEL it seems. I
gave the command mentioned in the Amber installation instructions file
(Since I am working in bash shell I used export command). But it doesn't
work. I don't know how to set. One more thing is, I don't know what is the
mpi version is in our server. Is the mpi version and its details are
essential for the testing process. If so, It would be very helpful, if
somebody could help me to know the mpi version and complete my installation
successfully. Thanks in advance. 

-- 
Live Life; Don't pass it
Bertrand.P.S.Russell 

-- 
Live Life; Don't pass it
Bertrand.P.S.Russell 

-- 
Live Life; Don't pass it
Bertrand.P.S.Russell 

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